Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_013840429.1 DESRU_RS01860 biosynthetic-type acetolactate synthase large subunit
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000215085.1:WP_013840429.1 Length = 553 Score = 580 bits (1496), Expect = e-170 Identities = 292/562 (51%), Positives = 388/562 (69%), Gaps = 11/562 (1%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M GA+IL+ +L E GVE ++GYPGG L IYD L+ + +HILVRHEQ A HAADGYA Sbjct: 2 KMSGAQILIDSLKEAGVETIFGYPGGQALPIYDALY-DSDLQHILVRHEQGAAHAADGYA 60 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 RA+GKVGV L TSGPG TN VTGIA AY+DS+PMV ITG VPT +G+D+FQE D GIT Sbjct: 61 RASGKVGVCLATSGPGATNLVTGIANAYMDSVPMVAITGQVPTFLLGRDSFQEVDITGIT 120 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 PI KHN++VKD++D+ +K+AF++A+TGRPGPV++DIPKD+S YE +++ Sbjct: 121 LPITKHNYIVKDIKDMGRIVKEAFYVASTGRPGPVLIDIPKDISSGEMDYERNGCLNLPG 180 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 YNP + + +A+ + + P IY GGGV+ + A EL++L+ PVT TLMGL Sbjct: 181 YNPPREAREDLVNQALRAIAESRCPVIYAGGGVISSGAHQELKKLSETLLAPVTVTLMGL 240 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKIIHI 317 G FPG +GMLGMHG+ AN A+ CD+LIA+G RFDDRV G F S A KIIHI Sbjct: 241 GGFPGDHPLSLGMLGMHGSKYANYAVCECDLLIAVGVRFDDRVTGKIESFASNA-KIIHI 299 Query: 318 DIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVDCL 377 DIDP+ + K V+VDIP+ G+VK VL +L+ +++A W E+I W+ Sbjct: 300 DIDPAEMGKNVQVDIPVTGDVKLVLNQLLERLEA-------RIPTAWQEKIAAWKKEYPF 352 Query: 378 KYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWINSGGLGTM 437 YDR+ E +KPQ ++ +I T G A I ++VGQHQMWAAQ+Y + +PR +I+SGGLGTM Sbjct: 353 DYDRTGETLKPQQIIREIDRQTSGQARITTEVGQHQMWAAQYYTYTKPRSFISSGGLGTM 412 Query: 438 GVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGMVRQ 497 G G P A+G++ A PE+ V I G+GSIQM IQEL+T + Y+ PV + +NNGYLGMVRQ Sbjct: 413 GYGFPAAIGVQVACPEETVFDIAGDGSIQMNIQELATAVNYELPVNVAIMNNGYLGMVRQ 472 Query: 498 WQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVFLDF 557 WQE+ Y+ RYS S M + PDFVKLAE+YG G R+ + +V P L+ A + + + V +DF Sbjct: 473 WQEMLYNRRYSQSEMKS-PDFVKLAESYGAEGYRITRKEEVTPVLQAAIQSR-KPVLMDF 530 Query: 558 QTDPTENVWPMVQAGKGISEML 579 +P ENV P V GKG++EML Sbjct: 531 VVEPEENVLPFVPPGKGLNEML 552 Lambda K H 0.319 0.135 0.407 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 906 Number of extensions: 31 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 585 Length of database: 553 Length adjustment: 36 Effective length of query: 549 Effective length of database: 517 Effective search space: 283833 Effective search space used: 283833 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
Align candidate WP_013840429.1 DESRU_RS01860 (biosynthetic-type acetolactate synthase large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00118.hmm # target sequence database: /tmp/gapView.770688.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00118 [M=557] Accession: TIGR00118 Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-268 877.0 0.0 2.8e-268 876.8 0.0 1.0 1 NCBI__GCF_000215085.1:WP_013840429.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013840429.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 876.8 0.0 2.8e-268 2.8e-268 1 554 [. 3 552 .. 3 553 .] 0.99 Alignments for each domain: == domain 1 score: 876.8 bits; conditional E-value: 2.8e-268 TIGR00118 1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 ++ga+il++slk+ gvet+fGyPGG+ lpiydalyds+l+hilvrheq+aahaadGyarasGkvGv+latsGP NCBI__GCF_000215085.1:WP_013840429.1 3 MSGAQILIDSLKEAGVETIFGYPGGQALPIYDALYDSDLQHILVRHEQGAAHAADGYARASGKVGVCLATSGP 75 79*********************************************************************** PP TIGR00118 74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146 Gatnlvtgia+ay+dsvP+v++tGqv+t l+G d+fqe+di+Gitlp+tkh+++vk+ +d+ +i+keaf++as NCBI__GCF_000215085.1:WP_013840429.1 76 GATNLVTGIANAYMDSVPMVAITGQVPTFLLGRDSFQEVDITGITLPITKHNYIVKDIKDMGRIVKEAFYVAS 148 ************************************************************************* PP TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219 tGrPGPvl+d+Pkd+++ e+++e + ++lpgy+p ++++ +++al +i++++ Pv+++GgGvi ++a++e NCBI__GCF_000215085.1:WP_013840429.1 149 TGRPGPVLIDIPKDISSGEMDYERNGCLNLPGYNPPREAREDLVNQALRAIAESRCPVIYAGGGVISSGAHQE 221 ************************************************************************* PP TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292 lk+l+e+l +pvt tl+GlG+fp dhpl+lgmlGmhG+k+an+av e+dlliavG+rfddrvtg++++fa++a NCBI__GCF_000215085.1:WP_013840429.1 222 LKKLSETLLAPVTVTLMGLGGFPGDHPLSLGMLGMHGSKYANYAVCECDLLIAVGVRFDDRVTGKIESFASNA 294 ************************************************************************* PP TIGR00118 293 kiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqk 365 kiihididPae+gknv+vdip+ Gd+k vl++ll++l+++ + W eki+ wkkey++ +d++ e++kPq+ NCBI__GCF_000215085.1:WP_013840429.1 295 KIIHIDIDPAEMGKNVQVDIPVTGDVKLVLNQLLERLEARIPTA--WQEKIAAWKKEYPFDYDRTGETLKPQQ 365 *************************************9988877..*************************** PP TIGR00118 366 vikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdg 438 +i+e+ ++++++a +tt+vGqhqmwaaq+y+++kpr+fi+sgGlGtmG+G+Paa+G++va peetv +++Gdg NCBI__GCF_000215085.1:WP_013840429.1 366 IIREIDRQTSGQARITTEVGQHQMWAAQYYTYTKPRSFISSGGLGTMGYGFPAAIGVQVACPEETVFDIAGDG 438 ************************************************************************* PP TIGR00118 439 sfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekp 511 s+qmn+qel+t+v+y++pv + i+nn +lGmv+qWqe++y++rys+++++s pdfvklae+yG++g ri+++ NCBI__GCF_000215085.1:WP_013840429.1 439 SIQMNIQELATAVNYELPVNVAIMNNGYLGMVRQWQEMLYNRRYSQSEMKS--PDFVKLAESYGAEGYRITRK 509 **************************************************6..******************** PP TIGR00118 512 eeleeklkealeskepvlldvevdkeeevlPmvapGagldelv 554 ee+ l+ a++s++pvl+d++v+ ee+vlP v+pG+gl+e++ NCBI__GCF_000215085.1:WP_013840429.1 510 EEVTPVLQAAIQSRKPVLMDFVVEPEENVLPFVPPGKGLNEML 552 *****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (557 nodes) Target sequences: 1 (553 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 30.74 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory